Merge branch 'geosampler_prechipping' into vers_working_branch

docs/conf.py

@@ -67,6 +67,7 @@
     ('py:class', 'torchvision.models._api.WeightsEnum'),
     ('py:class', 'torchvision.models.resnet.ResNet'),
     ('py:class', 'torchvision.models.swin_transformer.SwinTransformer'),
+    ('py:class', 'geopandas.GeoDataFrame'),
 ]
 
 
@@ -122,6 +123,7 @@
     'torch': ('https://pytorch.org/docs/stable', None),
     'torchmetrics': ('https://lightning.ai/docs/torchmetrics/stable/', None),
     'torchvision': ('https://pytorch.org/vision/stable', None),
+    'geopandas': ('https://geopandas.org/en/stable/', None),
 }
 
 # nbsphinx

docs/index.rst

@@ -29,6 +29,7 @@ torchgeo
    :caption: Tutorials
 
    tutorials/getting_started
+   tutorials/visualizing_samples
    tutorials/custom_raster_dataset
    tutorials/transforms
    tutorials/indices

docs/tutorials/visualizing_samples.ipynb

@@ -0,0 +1,159 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Visualizing Samples\n",
+    "\n",
+    "This tutorial shows how to visualize and save the extent of your samples before and during training. In this particular example, we compare a vanilla RandomGeoSampler with one bounded by multiple ROI's and show how easy it is to gain insight on the distribution of your samples."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import tempfile\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "from torch.utils.data import DataLoader\n",
+    "\n",
+    "from torchgeo.datasets import NAIP, stack_samples\n",
+    "from torchgeo.datasets.utils import download_url\n",
+    "from torchgeo.samplers import RandomGeoSampler\n",
+    "\n",
+    "\n",
+    "def run_epochs(dataset, sampler):\n",
+    "    dataloader = DataLoader(\n",
+    "        dataset, sampler=sampler, batch_size=1, collate_fn=stack_samples, num_workers=0\n",
+    "    )\n",
+    "    fig, ax = plt.subplots()\n",
+    "    num_epochs = 5\n",
+    "    for epoch in range(num_epochs):\n",
+    "        color = plt.cm.viridis(epoch / num_epochs)\n",
+    "        # sampler.chips.to_file(f'naip_chips_epoch_{epoch}') # Optional: save chips to file for display in GIS software\n",
+    "        ax = sampler.chips.plot(ax=ax, color=color)\n",
+    "        for sample in dataloader:\n",
+    "            pass\n",
+    "    plt.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Generate dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "naip_root = os.path.join(tempfile.gettempdir(), 'naip')\n",
+    "naip_url = (\n",
+    "    'https://naipeuwest.blob.core.windows.net/naip/v002/de/2018/de_060cm_2018/38075/'\n",
+    ")\n",
+    "tiles = ['m_3807511_ne_18_060_20181104.tif', 'm_3807512_sw_18_060_20180815.tif']\n",
+    "for tile in tiles:\n",
+    "    download_url(naip_url + tile, naip_root)\n",
+    "\n",
+    "naip = NAIP(naip_root)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "First we create the default sampler for our dataset (3 samples) and run it for 5 epochs and plot its results. Each color displays a different epoch, so we can see how the RandomGeoSampler has distributed it's samples for every epoch."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sampler = RandomGeoSampler(naip, size=1000, length=3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "run_epochs(naip, sampler)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we split our dataset by two bounding boxes and re-inspect the samples."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from torchgeo.datasets import roi_split\n",
+    "from torchgeo.datasets.utils import BoundingBox\n",
+    "\n",
+    "rois = [\n",
+    "    BoundingBox(440854, 442938, 4299766, 4301731, 0, np.inf),\n",
+    "    BoundingBox(449070, 451194, 4289463, 4291746, 0, np.inf),\n",
+    "]\n",
+    "datasets = roi_split(naip, rois)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined = datasets[0] | datasets[1]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sampler = RandomGeoSampler(combined, size=1000, length=3)\n",
+    "run_epochs(combined, sampler)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "cca",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

pyproject.toml

@@ -40,6 +40,8 @@ dependencies = [
     "einops>=0.3",
     # fiona 1.8.21+ required for Python 3.10 wheels
     "fiona>=1.8.21",
+    # geopandas 0.13.2 is the last version to support pandas 1.3, but has feather support
+    "geopandas>=0.13.2",
     # kornia 0.7.3+ required for instance segmentation support in AugmentationSequential
     "kornia>=0.7.3",
     # lightly 1.4.5+ required for LARS optimizer
@@ -58,6 +60,8 @@ dependencies = [
     "pandas>=1.3.3",
     # pillow 8.4+ required for Python 3.10 wheels
     "pillow>=8.4",
+    # pyarrow 12.0+ required for feather support
+    "pyarrow>=17.0.0",
     # pyproj 3.3+ required for Python 3.10 wheels
     "pyproj>=3.3",
     # rasterio 1.3+ required for Python 3.10 wheels

requirements/min-reqs.old

@@ -4,13 +4,15 @@ setuptools==61.0.0
 # install
 einops==0.3.0
 fiona==1.8.21
+geopandas==0.13.2
 kornia==0.7.3
 lightly==1.4.5
 lightning[pytorch-extra]==2.0.0
 matplotlib==3.5.0
 numpy==1.21.2
 pandas==1.3.3
 pillow==8.4.0
+pyarrow==17.0.0
 pyproj==3.3.0
 rasterio==1.3.0.post1
 rtree==1.0.0

requirements/required.txt

@@ -4,13 +4,15 @@ setuptools==75.1.0
 # install
 einops==0.8.0
 fiona==1.10.1
+geopandas==0.14.4
 kornia==0.7.3
 lightly==1.5.12
 lightning[pytorch-extra]==2.4.0
 matplotlib==3.9.2
 numpy==2.1.1
 pandas==2.2.3
 pillow==10.4.0
+pyarrow==17.0.0
 pyproj==3.6.1
 rasterio==1.3.11
 rtree==1.3.0

tests/data/samplers/filtering_4x4/filtering_4x4.cpg

@@ -0,0 +1 @@
+ISO-8859-1

tests/data/samplers/filtering_4x4/filtering_4x4.prj

@@ -0,0 +1 @@
+PROJCS["NAD_1983_BC_Environment_Albers",GEOGCS["GCS_North_American_1983",DATUM["D_North_American_1983",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Albers"],PARAMETER["False_Easting",1000000.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",-126.0],PARAMETER["Standard_Parallel_1",50.0],PARAMETER["Standard_Parallel_2",58.5],PARAMETER["Latitude_Of_Origin",45.0],UNIT["Meter",1.0]]

tests/datamodules/test_geo.py

@@ -7,6 +7,7 @@
 import pytest
 import torch
 from _pytest.fixtures import SubRequest
+from geopandas import GeoDataFrame
 from lightning.pytorch import Trainer
 from matplotlib.figure import Figure
 from rasterio.crs import CRS
@@ -182,7 +183,7 @@ def test_zero_length_sampler(self) -> None:
         dm = CustomGeoDataModule()
         dm.dataset = CustomGeoDataset()
         dm.sampler = RandomGeoSampler(dm.dataset, 1, 1)
-        dm.sampler.length = 0
+        dm.sampler.chips = GeoDataFrame()
         msg = r'CustomGeoDataModule\.sampler has length 0.'
         with pytest.raises(MisconfigurationException, match=msg):
             dm.train_dataloader()